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@ -254,49 +254,43 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># NOT RUN {</span>
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<span class='co'># septic_patients is a data set available in the AMR package. It is true, genuine data.</span>
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?<span class='no'>septic_patients</span>
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<pre class="examples"><div class='input'><span class='co'># septic_patients is a data set available in the AMR package. It is true, genuine data.</span>
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?<span class='no'>septic_patients</span></div><div class='output co'>#> <span class='message'>Rendering development documentation for 'septic_patients'</span></div><div class='input'>
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<span class='co'># Calculate resistance</span>
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<span class='fu'>portion_R</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>portion_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>portion_R</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)</div><div class='output co'>#> [1] 0.5827645</div><div class='input'><span class='fu'>portion_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)</div><div class='output co'>#> [1] 0.5853242</div><div class='input'>
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<span class='co'># Or susceptibility</span>
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<span class='fu'>portion_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>portion_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>portion_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)</div><div class='output co'>#> [1] 0.4146758</div><div class='input'><span class='fu'>portion_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)</div><div class='output co'>#> [1] 0.4172355</div><div class='input'>
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<span class='co'># Do the above with pipes:</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_R</span>(<span class='no'>amox</span>)
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_IR</span>(<span class='no'>amox</span>)
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>amox</span>)
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_SI</span>(<span class='no'>amox</span>)
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_R</span>(<span class='no'>amox</span>)</div><div class='output co'>#> [1] 0.5827645</div><div class='input'><span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_IR</span>(<span class='no'>amox</span>)</div><div class='output co'>#> [1] 0.5853242</div><div class='input'><span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>amox</span>)</div><div class='output co'>#> [1] 0.4146758</div><div class='input'><span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_SI</span>(<span class='no'>amox</span>)</div><div class='output co'>#> [1] 0.4172355</div><div class='input'>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>),
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<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>)) <span class='co'># n_rsi works like n_distinct in dplyr</span>
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<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>)) <span class='co'># n_rsi works like n_distinct in dplyr</span></div><div class='output co'>#> <span style='color: #949494;'># A tibble: 4 x 3</span><span>
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#> hospital_id p n
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#> </span><span style='color: #949494;font-style: italic;'><fct></span><span> </span><span style='color: #949494;font-style: italic;'><dbl></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span>
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#> </span><span style='color: #BCBCBC;'>1</span><span> A 0.860 207
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#> </span><span style='color: #BCBCBC;'>2</span><span> B 0.760 499
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#> </span><span style='color: #BCBCBC;'>3</span><span> C 0.688 202
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#> </span><span style='color: #BCBCBC;'>4</span><span> D 0.830 501</div><div class='input'>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>portion_R</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
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<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>portion_I</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
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<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
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<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>), <span class='co'># works like n_distinct in dplyr</span>
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<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='http://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span>
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<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='http://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span></div><div class='output co'>#> </span><span style='color: #949494;'># A tibble: 4 x 6</span><span>
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#> hospital_id R I S n total
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#> </span><span style='color: #949494;font-style: italic;'><fct></span><span> </span><span style='color: #949494;font-style: italic;'><chr></span><span> </span><span style='color: #949494;font-style: italic;'><chr></span><span> </span><span style='color: #949494;font-style: italic;'><chr></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span>
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#> </span><span style='color: #BCBCBC;'>1</span><span> A 12.6% 1.4% 86.0% 207 321
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#> </span><span style='color: #BCBCBC;'>2</span><span> B 17.0% 7.0% 76.0% 499 663
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#> </span><span style='color: #BCBCBC;'>3</span><span> C 20.3% 10.9% 68.8% 202 254
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#> </span><span style='color: #BCBCBC;'>4</span><span> D 15.2% 1.8% 83.0% 501 762</div><div class='input'>
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<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
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<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>amcl</span>) <span class='co'># S = 67.1%</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amcl</span>) <span class='co'># n = 1576</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>gent</span>) <span class='co'># S = 74.0%</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>gent</span>) <span class='co'># n = 1855</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>) <span class='co'># S = 92.0%</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amcl</span>, <span class='no'>gent</span>) <span class='co'># n = 1517</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>amcl</span>) <span class='co'># S = 67.1%</span></div><div class='output co'>#> [1] 0.7062363</div><div class='input'><span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amcl</span>) <span class='co'># n = 1576</span></div><div class='output co'>#> [1] 1828</div><div class='input'>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>gent</span>) <span class='co'># S = 74.0%</span></div><div class='output co'>#> [1] 0.7396226</div><div class='input'><span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>gent</span>) <span class='co'># n = 1855</span></div><div class='output co'>#> [1] 1855</div><div class='input'>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>) <span class='co'># S = 92.0%</span></div><div class='output co'>#> [1] 0.9210074</div><div class='input'><span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amcl</span>, <span class='no'>gent</span>) <span class='co'># n = 1517</span></div><div class='output co'>#> [1] 1747</div><div class='input'>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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@ -305,21 +299,43 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
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<span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>gent</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
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<span class='kw'>genta_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>gent</span>),
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<span class='kw'>combination_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='no'>gent</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
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<span class='kw'>combination_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>cipr</span>, <span class='no'>gent</span>))
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<span class='kw'>combination_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>cipr</span>, <span class='no'>gent</span>))</div><div class='output co'>#> </span><span style='color: #949494;'># A tibble: 4 x 7</span><span>
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#> hospital_id cipro_p cipro_n genta_p genta_n combination_p combination_n
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#> </span><span style='color: #949494;font-style: italic;'><fct></span><span> </span><span style='color: #949494;font-style: italic;'><chr></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><chr></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><chr></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span>
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#> </span><span style='color: #BCBCBC;'>1</span><span> A 86.0% 207 76.0% 300 95.0% 202
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#> </span><span style='color: #BCBCBC;'>2</span><span> B 76.0% 499 71.5% 606 91.4% 488
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#> </span><span style='color: #BCBCBC;'>3</span><span> C 68.8% 202 75.8% 240 91.5% 201
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#> </span><span style='color: #BCBCBC;'>4</span><span> D 83.0% 501 74.6% 709 95.0% 499</div><div class='input'>
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<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
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<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> Interpretation Antibiotic Value
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#> 1 S amox 0.414675768
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#> 2 I amox 0.002559727
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#> 3 R amox 0.582764505
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#> 4 S cipr 0.789212207
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#> 5 I cipr 0.048970901
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#> 6 R cipr 0.161816891</div><div class='input'>
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<span class='co'># It also supports grouping variables</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> </span><span style='color: #949494;'># A tibble: 24 x 4</span><span>
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#> Interpretation hospital_id Antibiotic Value
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#> </span><span style='color: #949494;font-style: italic;'><ord></span><span> </span><span style='color: #949494;font-style: italic;'><fct></span><span> </span><span style='color: #949494;font-style: italic;'><chr></span><span> </span><span style='color: #949494;font-style: italic;'><dbl></span><span>
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#> </span><span style='color: #BCBCBC;'> 1</span><span> S A amox 0.42
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#> </span><span style='color: #BCBCBC;'> 2</span><span> S B amox 0.378
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#> </span><span style='color: #BCBCBC;'> 3</span><span> S C amox 0.373
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#> </span><span style='color: #BCBCBC;'> 4</span><span> S D amox 0.454
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#> </span><span style='color: #BCBCBC;'> 5</span><span> I A amox 0
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#> </span><span style='color: #BCBCBC;'> 6</span><span> I B amox 0.002</span><span style='text-decoration: underline;'>68</span><span>
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#> </span><span style='color: #BCBCBC;'> 7</span><span> I C amox 0
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#> </span><span style='color: #BCBCBC;'> 8</span><span> I D amox 0.004</span><span style='text-decoration: underline;'>07</span><span>
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#> </span><span style='color: #BCBCBC;'> 9</span><span> R A amox 0.580
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#> </span><span style='color: #BCBCBC;'>10</span><span> R B amox 0.619
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#> </span><span style='color: #949494;'># ... with 14 more rows</span><span></div><div class='input'>
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<span class='co'># }</span><span class='co'># NOT RUN {</span>
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</div></span><span class='co'># NOT RUN {</span>
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<span class='co'># calculate current empiric combination therapy of Helicobacter gastritis:</span>
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<span class='no'>my_table</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
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